All v6s are 4l60s, only v8s got 4l65s. There are some tailshaft differences between vt and vx/y/z though, some have donuts some have uni joints.
The sumps should be fine.
Not sure about the chips and ecus, VATS will need to be relinked (tech2) or disabled if you swap ecus, im sure it could be made to work though.
Exhaust will fit fine.
There are differenes in the fuel system on s/c cars, easiest way would be find a s/c vy calais, should be an easy swap then.
Best way would be to grab the factory service manual and get busy reading, it explains a lot of the changes made over the years and differences between s/c and normal v6. You can find it on thepiratebay, search for vt commodore (covers vt/vx/vy, 679mb cd image file).